R/gen_bib.R

In NicolasJBM/writer: Functions and interfaces to support academic writing with R

#' Function for creatng the reference file of the  markdown documents in the working directory.
#' @return A bib file.
#' @importFrom tibble column_to_rownames
#' @importFrom tibble rownames_to_column
#' @importFrom tibble remove_rownames
#' @importFrom dplyr filter
#' @importFrom dplyr mutate
#' @importFrom dplyr %>%
#' @importFrom dplyr bind_rows
#' @importFrom dplyr group_by
#' @importFrom dplyr ungroup
#' @importFrom dplyr sample_n
#' @importFrom dplyr mutate_all
#' @importFrom tidyr unnest
#' @importFrom purrr map
#' @importFrom stringr str_detect
#' @importFrom stringr str_extract_all
#' @importFrom stringr str_replace_all
#' @importFrom stats na.omit
#' @importFrom utils read.csv
#' @importFrom utils write.csv
#' @importFrom utils installed.packages
#' @importFrom RefManageR ReadBib
#' @importFrom readr read_file
#' @importFrom RefManageR WriteBib
#' @importFrom RefManageR as.BibEntry
#' @export


gen_bib <- function() {
  
  # Bind variables
  year <- NULL
  number <- NULL
  volume <- NULL
  key <- NULL
  title <- NULL
  abstract <- NULL
  Freq <- NULL
  
  # Obtain references
  if ("bibliogr" %in% row.names(installed.packages())){
    biblio <- bibliogr::references
  } else {
    biblio <- rstudioapi::selectFile(caption = "Select the database of references")
    
    if (stringr::str_detect(biblio, ".bib$")) {
      bilbio <- ReadBib(biblio) %>%
        as.data.frame() %>%
        rownames_to_column("key") %>%
        mutate(
          year = as.integer(year),
          number = as.integer(number),
          volume = as.integer(volume)
        )
    } else {
      biblio <- read.csv(biblio, stringsAsFactors = FALSE)
    }
  }
  
  
  # Gather citations
  files <- list.files(getwd())
  rmdfiles <- tibble::tibble(rmdfiles = files[stringr::str_detect(files, ".Rmd$")])
  
  if (nrow(rmdfiles) > 0){
    content <- rmdfiles %>%
      dplyr::mutate(text = purrr::map(rmdfiles, read_file)) %>%
      tidyr::unnest()
    content <- paste(as.character(unlist(content$text)), collaspe = " ")   
  }
  
  selection <- content %>%
    str_extract_all("@\\w+") %>%
    unlist() %>%
    str_remove_all("@") %>%
    unique()
  
  # Create bib file
  if (length(selection) > 0 & nrow(biblio) > 0){
    basebib <- biblio %>%
      dplyr::filter(key %in% selection) %>%
      as.data.frame()
    
    bib <- basebib %>%
      mutate_all(str_replace_all, pattern = "&", replacement = "\\\\&") %>%
      mutate(
        title = paste0("{", title,"}"),
        abstract = paste0("{", abstract,"}")
      ) %>%
      unique() %>%
      group_by(key) %>%
      sample_n(1) %>%
      ungroup() %>%
      as.data.frame()
    
    journal_rank <- bib$journal %>%
      table() %>%
      as.data.frame() %>%
      arrange(-Freq)
    write.csv(journal_rank, "journal_rank.csv", row.names = FALSE)
    
    author_rank <- bib$author %>%
      stringr::str_extract_all("^(.*?), | and(.*?),") %>%
      unlist() %>%
      stringr::str_remove_all(" and ") %>%
      str_remove_all(",") %>%
      trimws() %>%
      table() %>%
      as.data.frame() %>%
      arrange(-Freq)
    write.csv(author_rank, "author_rank.csv", row.names = FALSE)
    
    bib <- bib %>%
      split(f = bib$key) %>%
      as.BibEntry() %>%
      WriteBib(file = "ref.bib", append = FALSE)
  }
}